[R-pkg-devel] CRAN note about \href{https://doi.org/...}{label} in Rd files

Hi,

When running R CMD check on R-devel, a CRAN note appears about
\href{https://doi.org/...}{label} in Rd files. Like:

Found the following URLs which should use \doi (with the DOI name only):
  ? File ?read_GRTSmh.Rd?:
  ??? https://doi.org/10.5281/zenodo.2611233
  ??? https://doi.org/10.5281/zenodo.3354403
  ? File ?read_GRTSmh_base4frac.Rd?:
  ??? https://doi.org/10.5281/zenodo.3354401

(Full output is at
https://github.com/inbo/n2khab/runs/2219662325?check_suite_focus=true#step:10:35)

The note does not appear in R 4.0.4.

The cause is documentation hyperlinks to doi.org, ** inside \href{} **:

./man/read_GRTSmh.Rd:42:\href{https://doi.org/10.5281/zenodo.2611233}{Zenodo},
is a monolayered GeoTIFF
./man/read_GRTSmh.Rd:73:\href{https://doi.org/10.5281/zenodo.3354403}{Zenodo},
and can only be
./man/read_GRTSmh_base4frac.Rd:33:\href{https://doi.org/10.5281/zenodo.3354401}{Zenodo}.
./man/read_GRTSmh_diffres.Rd:45:at
\href{https://doi.org/10.5281/zenodo.3354405}{Zenodo}), composed of
./man/read_habitatmap_stdized.Rd:68:\href{https://doi.org/10.5281/zenodo.3355192}{Zenodo},
that
./man/read_habitatmap_terr.Rd:117:\href{https://doi.org/10.5281/zenodo.3468948}{Zenodo},
that contains:
./man/read_habitatquarries.Rd:70:\href{https://doi.org/10.5281/zenodo.4072967}{Zenodo},
that contains:
./man/read_habitatsprings.Rd:83:\href{https://doi.org/10.5281/zenodo.3550994}{Zenodo}.
./man/read_soilmap.Rd:225:\href{https://doi.org/10.5281/zenodo.3732903}{Zenodo}.
./man/read_watercourse_100mseg.Rd:73:\href{https://doi.org/10.5281/zenodo.4452577}{Zenodo},
and contains two
./man/read_watercourse_100mseg.Rd:83:\href{https://doi.org/10.5281/zenodo.4420904}{\code{watercourses}}
data
./man/read_watersurfaces_hab.Rd:66:\href{https://doi.org/10.5281/zenodo.3386857}{watersurface
map of Flanders}.
./man/read_watersurfaces_hab.Rd:71:\href{https://doi.org/10.5281/zenodo.3374645}{Zenodo},
that contains:


Can this be resolved using \doi{} as suggested, while still resulting in
a working link to doi.org? I didn't find a way to do that.

Perhaps a 'https://doi.org' address which does not show as such in the
documentation (because of the clickable label) should still be allowed.


With regards

Floris Vanderhaeghe

I just tried \doi{10.5281/zenodo.2611233} and it worked. 

When running R CMD check on R-devel, a CRAN note appears about \href{https://doi.org/...}{label} in Rd files...
... Can this be resolved using \doi{} as suggested, while still resulting in a working link to doi.org? I didn't find a way to do that.

I just tried \doi{10.5281/zenodo.2611233} and it worked.

Sure, but what about making a hyperlink to
https://doi.org/10.5281/zenodo.2611233 while showing "text" in the
documentation, as in \href{wwwaddress}{text}. I assume the CRAN note
appears because it wants literal DOI strings in the documentation to be
specified with \doi{}. However with \href{} the DOI string remains hidden.

href{\doi{10.5281/zenodo.2611233}}{text} is a non-functional link while
\href{https://doi.org/10.5281/zenodo.2611233}{text} is functional.

On 30/03/2021 10:39 a.m., Floris Vanderhaeghe wrote:

I just tried \doi{10.5281/zenodo.2611233} and it worked.

Sure, but what about making a hyperlink to
https://doi.org/10.5281/zenodo.2611233 while showing "text" in the
documentation, as in \href{wwwaddress}{text}. I assume the CRAN note
appears because it wants literal DOI strings in the documentation to be
specified with \doi{}. However with \href{} the DOI string remains hidden.

href{\doi{10.5281/zenodo.2611233}}{text} is a non-functional link while
\href{https://doi.org/10.5281/zenodo.2611233}{text} is functional.

No, I don't think there's currently any way to do that.  Your choices
are probably to link to whatever the DOI links to, e.g.
\href{https://zenodo.org/record/2682323}{text} and live with the fact
that the URL might change tomorrow, or show the DOI.

On 30/03/2021 12:36 p.m., Duncan Murdoch wrote:

On 30/03/2021 10:39 a.m., Floris Vanderhaeghe wrote:

I just tried \doi{10.5281/zenodo.2611233} and it worked.

Sure, but what about making a hyperlink to
https://doi.org/10.5281/zenodo.2611233 while showing "text" in the
documentation, as in \href{wwwaddress}{text}. I assume the CRAN note
appears because it wants literal DOI strings in the documentation to be
specified with \doi{}. However with \href{} the DOI string remains 
hidden.

href{\doi{10.5281/zenodo.2611233}}{text} is a non-functional link while
\href{https://doi.org/10.5281/zenodo.2611233}{text} is functional.

No, I don't think there's currently any way to do that.? Your choices
are probably to link to whatever the DOI links to, e.g.
\href{https://zenodo.org/record/2682323}{text} and live with the fact
that the URL might change tomorrow, or show the DOI.

One other suggestion:? define your own \doi{} macro.? The current 
definition (from R_HOME/share/Rd/macros/system.Rd) is

\newcommand{\doi}{\Sexpr[results=rd,stage=build]{tools:::Rd_expr_doi("#1")}} 


You could make a two-argument variant on this.? You could even submit 
it as a patch on Bugzilla if you think others would like it.

Duncan Murdoch

This is a recent addition to R checks. I am pretty sure that \doi{} with the suggested syntax does produce proper links in the documentation.

Georgi Boshnakov